Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167961.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_220, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48538
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2806 original size:14 final size:15
Alignment explanation
Indices: 2787--2821 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2777 AAATAGTCAT
2787 TATTTT-TTATGCTC
1 TATTTTCTTATGCTC
2801 TATTTTCGTTATGCTC
1 TATTTTC-TTATGCTC
2817 TATTT
1 TATTT
2822 GGATGATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
16 13 0.68
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.63
Consensus pattern (15 bp):
TATTTTCTTATGCTC
Found at i:6781 original size:163 final size:163
Alignment explanation
Indices: 6511--6842 Score: 637
Period size: 163 Copynumber: 2.0 Consensus size: 163
6501 ATTAGGTGAA
6511 CATTTTTGTTAGGATCTGCAGCCTTTTCAATGATTTGCAATAGACTTATTCTGTTTGGTTGTGGC
1 CATTTTTGTTAGGATCTGCAGCCTTTTCAATGATTTGCAATAGACTTATTCTGTTTGGTTGTGGC
6576 CTGTACGTGTAAAATGCTATGCAAGCTCTGTTGTCTACTTGTCTGGGTGCTTTTAGCGTCTGTCA
66 CTGTACGTGTAAAATGCTATGCAAGCTCTGTTGTCTACTTGTCTGGGTGCTTTTAGCGTCTGTCA
6641 CCTATTGTTGATCAACACATGCACGTGATGCTT
131 CCTATTGTTGATCAACACATGCACGTGATGCTT
*
6674 CATTTTTGTTAGGATTTGCAGCCTTTTCAATGATTTGCAATAGACTTATTCTGTTTGGTTGTGGC
1 CATTTTTGTTAGGATCTGCAGCCTTTTCAATGATTTGCAATAGACTTATTCTGTTTGGTTGTGGC
6739 CTGTACGTGTAAAATGCTATGCAAGCTCTGTTGTCTACTTGTCTGGGTGCTTTTAGCGTCTGTCA
66 CTGTACGTGTAAAATGCTATGCAAGCTCTGTTGTCTACTTGTCTGGGTGCTTTTAGCGTCTGTCA
* *
6804 CCTATTGTTGATCAACACATGCATGTGATGGTT
131 CCTATTGTTGATCAACACATGCACGTGATGCTT
6837 CATTTT
1 CATTTT
6843 GGGTTAGATT
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 166 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (163 bp):
CATTTTTGTTAGGATCTGCAGCCTTTTCAATGATTTGCAATAGACTTATTCTGTTTGGTTGTGGC
CTGTACGTGTAAAATGCTATGCAAGCTCTGTTGTCTACTTGTCTGGGTGCTTTTAGCGTCTGTCA
CCTATTGTTGATCAACACATGCACGTGATGCTT
Found at i:14171 original size:877 final size:874
Alignment explanation
Indices: 12246--15063 Score: 4362
Period size: 877 Copynumber: 3.3 Consensus size: 874
12236 ATTCTAAAAC
*
12246 TTAATTTTGACATGCATTG-GGCTTGAATGCTTAAAAGGAAGATTATTTCGTTTTGCTGGATTCT
1 TTAATTTTGACATGCATTGTGG-TTGAATGCTTAAAAGGAAGATTATTTCTTTTTGCTGGATTCT
* * * *
12310 TTGAAATTCTAAATATATGTTGTCATAGTCTCTCAGTTGGTGTCTTTTTCATTGAAATTGTGTCT
65 TTGAAACTCTAAATATATGTTGTCATAGGCTCTCAGTTGGTGTCTTTTTCATTGAGATTGTCTCT
* * * *
12375 TGATTCTTCTTGTTTTATTTTTAAA-CTTTTACATAAATTAGGGCTTTGTAACTTTACTTTGAAA
130 GGATTCTTCTTGTGTCATTTTTAAATC-TTTACATAAATTAGGGCTTTGTAACTTTACTTTGGAA
*
12439 AATTCCTTGGGTTGTTCTTCCTTTAGTGTGGTTTGTGATTCGTTGGTCTCTATTAAACTTATGCG
194 AATTCCTTGGGTTGTTCTTCCTTTAGTGTGGTTTGTGATTCGTTGGTCTCTATGAAACTTATGCG
*
12504 CGATGTGCTCCAAGAACGACTTGCAGTGTAGGGGGAATTAAGGATTCTAAAGTTGTATGTGTGTA
259 CTATGTGCTCCAAGAACGACTTGCAGTGTAGGGGGAATTAAGGATTCTAAAGTTGTATGTGTGTA
*
12569 GGATTTAAGGATTAAAAATTTGTGTGGCTGTGTATGGGAGTTTCCTTGTTTTTCTCTTTGTGTGT
324 GGATTTAAGGATTAAAAATTTGTGTGGCTGTGTATGGGAGTTTCCTTGTTTTTCTCTTTGTGTGC
12634 TCTAAGCTAATGGCTTGCATGATTAGCTGAATTCAATTTCTGTGCCTGA--TGTGTGTAGGTGTA
389 TCTAAGCTAATGGCTTGCATGATTAGCTGAATTCAATTTCTGTGCCTGATGTGTGTGTAGGT-T-
* *
12697 TTTTGGGAGTTTTTTGTTTTGTTGATTTCACTC---TGTTACAGAACAGGTTGGTTTGTTGGGTT
452 TTTTGGGAGTTTTTTGTTTTGTTGATTTCACTCTTTTGTTATAGAATAGGTTGGTTTGTTGGGTT
12759 CAATTTCTGAAACTTAATTTTGACATGCATTGTGGTCAAATGTTTAAAAGGAAGATTATTTCCTT
517 CAATTTCTGAAACTTAATTTTGACATGCATTGTGGTCAAATGTTTAAAAGGAAGATTATTTCCTT
*
12824 TTGCTGGATTCTTTGAAACTCTAAATATGTGTATGGGAGTTTCCTTGTTGCTTTGTAGTGTAGGG
582 TTGTTGGATTCTTTGAAACTCTAAATATGTGTATGGGAGTTTCCTTGTTGCTTTGTAGTGTAGGG
12889 GGAATTAAGGATTCTAAATTTCTATGGTTGTGTAGCATTTAAGGATTAAAAATTTATGTGGCTGT
647 GGAATTAAGGATTCTAAATTTCTATGGTTGTGTAGCATTTAAGGATTAAAAA-TT-TGTGGCTGT
*
12954 GTGGTAT-GACAGTATTCCTGTTGTTTTCTCCTTGTGTGCTTCAAGCAGTGAATTCAATTTCTGT
710 GT-GTATGGA-AGTTTTCCTGTTGTTTTCTCCTTGTGTGCTTCAAGCAGTGAATTCAATTTCTGT
13018 GCCTCTTGTGTGTGTAGGTATGTGTTTAGGGAGGGTTTTATTTTGTTGGTTTCACTCTATTTGTT
773 GCCTC-TGTGTGTGTAGGTATGTGTTTAGGGAGGGTTTTATTTTGTTGGTTTCACTCTATTTGTT
* *
13083 ACAGGACAGATTGGTTTGCTAGGTTCAATTTCTGTAAT
837 ACAGGGCAGATTGGTTTGCTAGGTTCAATTTTTGTAAT
* *
13121 TTAATTTTGACATGCATTGTGGTTGAATGCTTGAAAGGAAGATTATTTCCTTTTGCTGGATTCTT
1 TTAATTTTGACATGCATTGTGGTTGAATGCTTAAAAGGAAGATTATTTCTTTTTGCTGGATTCTT
13186 TGAAACTCTAAATATATGTTGTCATAGGCTCTCAGTTGGTGTCTTTTTCATTGAGATTGTCTCTG
66 TGAAACTCTAAATATATGTTGTCATAGGCTCTCAGTTGGTGTCTTTTTCATTGAGATTGTCTCTG
*
13251 GATTCTTCTTGTGTCATTTTTAAATTTTTACATAAATTAGGGCTTTGTAACTTTACTTTGGAAAA
131 GATTCTTCTTGTGTCATTTTTAAATCTTTACATAAATTAGGGCTTTGTAACTTTACTTTGGAAAA
13316 TTCCTTGGGTTGTTCTTCCTTTAGTGTGGTTTGTGATTCGTTGGTCTCTATGAAACTTATGCGCT
196 TTCCTTGGGTTGTTCTTCCTTTAGTGTGGTTTGTGATTCGTTGGTCTCTATGAAACTTATGCGCT
13381 ATGTGCTCCAAGAACGACTTGCAGTGTAGGGGGAATTAAGGATTCTAAAGTTGTATGTGTGTAGG
261 ATGTGCTCCAAGAACGACTTGCAGTGTAGGGGGAATTAAGGATTCTAAAGTTGTATGTGTGTAGG
13446 ATTTAAGGATTAAAAATTTGTGTGGCTGTGTATGGGAGTTTCCTTGTTTTTCTCTTTGTGTGCTC
326 ATTTAAGGATTAAAAATTTGTGTGGCTGTGTATGGGAGTTTCCTTGTTTTTCTCTTTGTGTGCTC
13511 TAAGCTAATGGCTTGCATGATTAGCTGAATTCAATTTCTGTGCCTGATGTGTGTGTAGGTATTTT
391 TAAGCTAATGGCTTGCATGATTAGCTGAATTCAATTTCTGTGCCTGATGTGTGTGTAGG--TTTT
13576 TTGGGAGTTTTTTGTTTTGTTGATTTCACTCTGTTTGTTATAGAATAGGTTGGTTTGTTGGGTTC
454 TTGGGAGTTTTTTGTTTTGTTGATTTCACTCT-TTTGTTATAGAATAGGTTGGTTTGTTGGGTTC
* *
13641 AATTTCTGAAACTTAATTTTGACATGCATTGTAGTCAAATGTTTAAAAGGAAGATTATTTCTTTT
518 AATTTCTGAAACTTAATTTTGACATGCATTGTGGTCAAATGTTTAAAAGGAAGATTATTTCCTTT
* *
13706 TGTTGGATTCTTTGAAACTCTAAATATGTGTATGGGAGTTTCCTTGTTGCTTTGCAATGTAGGGG
583 TGTTGGATTCTTTGAAACTCTAAATATGTGTATGGGAGTTTCCTTGTTGCTTTGTAGTGTAGGGG
* *
13771 GAATCAAGGATTCTAAATTTTTATGGTTGTGTAGCATTTAAGGATTAAAAATTTGTGGCTGTGTG
648 GAATTAAGGATTCTAAATTTCTATGGTTGTGTAGCATTTAAGGATTAAAAATTTGTGGCTGTGTG
* * * *
13836 TATGGAAGTTTTCCTGTTGTTTTTCTCCTTGTGTGCTTCGAGCAGTGAATTAAATTTCTGCGACT
713 TATGGAAGTTTTCCTGTTG-TTTTCTCCTTGTGTGCTTCAAGCAGTGAATTCAATTTCTGTGCCT
*
13901 C-GTGTGTGTAGGTATGTGTTTAGGGAGGGTTTTATTTTGTTGGTTTCACTCTATTTGTTGCAGG
777 CTGTGTGTGTAGGTATGTGTTTAGGGAGGGTTTTATTTTGTTGGTTTCACTCTATTTGTTACAGG
13965 GCAGATTGGTTTGCTAGGTTCAATTTTTGTAAT
842 GCAGATTGGTTTGCTAGGTTCAATTTTTGTAAT
* * *
13998 TTAATTTTGACATGCATTGTGGTTGAATGCTTAAAAGAAATATTATTTCTTTTTGCTGAATTCTT
1 TTAATTTTGACATGCATTGTGGTTGAATGCTTAAAAGGAAGATTATTTCTTTTTGCTGGATTCTT
* * *
14063 TGAAACTTTAAATATATGTTGTCATAGGCTTTCAGTTGGTGTCTTTCTT-ATTGAGATTCTCTCT
66 TGAAACTCTAAATATATGTTGTCATAGGCTCTCAGTTGGTGTCTTT-TTCATTGAGATTGTCTCT
*
14127 GGATTCTTTTTGTGTCATTTTTAAATCTTTACATAAATTAGGGCTTTGTAACTTTACTTTGGAAA
130 GGATTCTTCTTGTGTCATTTTTAAATCTTTACATAAATTAGGGCTTTGTAACTTTACTTTGGAAA
** * *
14192 ATTCCTCAGGTTGTTCTTCTTTTAGTGTGGTTTGTGATTCGTTGGTCTCTATGAAACTTATGCGT
195 ATTCCTTGGGTTGTTCTTCCTTTAGTGTGGTTTGTGATTCGTTGGTCTCTATGAAACTTATGCGC
* * *
14257 TATGTGTTCCAAGAATGACTTGTAGTGTAGGGGGAATTAAGGATTCTAAAGTTGTATGTGTGTAG
260 TATGTGCTCCAAGAACGACTTGCAGTGTAGGGGGAATTAAGGATTCTAAAGTTGTATGTGTGTAG
* * *
14322 GATTTAAGGATTAAATATTTATGTGGTTGTGTATGGGAGTTTCCTTGTTTTTCTCTTTGTGTGCT
325 GATTTAAGGATTAAAAATTTGTGTGGCTGTGTATGGGAGTTTCCTTGTTTTTCTCTTTGTGTGCT
* * *
14387 CTAAGCTAATGGCTTGCATGATTAGTTAAATTCAATTTCTGTGCCTAATGTGTGTGTAGG-----
390 CTAAGCTAATGGCTTGCATGATTAGCTGAATTCAATTTCTGTGCCTGATGTGTGTGTAGGTTTTT
* *
14447 T-GTA--TTTTTG----G--GA-GT---T-TTTTGTT-T----T--GTTGG---G-T---TTCAA
455 TGGGAGTTTTTTGTTTTGTTGATTTCACTCTTTTGTTATAGAATAGGTTGGTTTGTTGGGTTCAA
14484 TTTCTGAAACTTAATTTTGACATGCATTGTGGTCAAATG--T--AAGGAAGATTATTTCCTTTTG
520 TTTCTGAAACTTAATTTTGACATGCATTGTGGTCAAATGTTTAAAAGGAAGATTATTTCCTTTTG
* * * * *
14545 TTGGATTCTTTGAAACTCTAAATATGTGTA-AGGAGTTTTCTTGTTGTTTTGTAGTGTAAGGTGA
585 TTGGATTCTTTGAAACTCTAAATATGTGTATGGGAGTTTCCTTGTTGCTTTGTAGTGTAGGGGGA
*
14609 ATTAAGGATTCTAAATTTCTATGGTTGTGTAGCATTTAATGATTAAAAATTTGTGGC--TGTGTA
650 ATTAAGGATTCTAAATTTCTATGGTTGTGTAGCATTTAAGGATTAAAAATTTGTGGCTGTGTGTA
* * *
14672 TGGGAGTTTCCCTGTTGCTTTTCTCCTTGTGTGCTTCAAGCAGTTAATTCAATTTCTGTGCCTCT
715 TGGAAGTTTTCCTGTTG-TTTTCTCCTTGTGTGCTTCAAGCAGTGAATTCAATTTCTGTGCCTC-
* * * *
14737 TGTGTGAGTAGGTATATGTTTAGGGAGGTTTTTATTTTGTTGGTTTCACTCTATTTGTTACAGAG
778 TGTGTGTGTAGGTATGTGTTTAGGGAGGGTTTTATTTTGTTGGTTTCACTCTATTTGTTACAGGG
*
14802 CAGATTGGTTTGTTAGGTTTC-ATTTTTGTAAT
843 CAGATTGGTTTGCTAGG-TTCAATTTTTGTAAT
* * * *
14834 TTAATTATGACGTGCATTATGGTTGAATGCTTGAAAGGAAGATTATTTCTTTTTGCTGGATTCTT
1 TTAATTTTGACATGCATTGTGGTTGAATGCTTAAAAGGAAGATTATTTCTTTTTGCTGGATTCTT
* *
14899 TGAAACTCTAAATATATGTTGTCATATGCTCTC----GGTGTCTTTCTCATTGAGATTGTCTCTG
66 TGAAACTCTAAATATATGTTGTCATAGGCTCTCAGTTGGTGTCTTTTTCATTGAGATTGTCTCTG
* * * *
14960 GATTTTTCTTGTGTCATTTTTAAATTTTTACATAAATTAGGGCTTTATAATTTTACTTT-GAAAA
131 GATTCTTCTTGTGTCATTTTTAAATCTTTACATAAATTAGGGCTTTGTAACTTTACTTTGGAAAA
* *
15024 TTTTCTTGGGTTATTCTTCCTTTAGTGTGGTTTGTGATTC
196 -TTCCTTGGGTTGTTCTTCCTTTAGTGTGGTTTGTGATTC
15064 AAGCAGTGAA
Statistics
Matches: 1821, Mismatches: 104, Indels: 79
0.91 0.05 0.04
Matches are distributed among these distances:
831 6 0.00
832 112 0.06
834 62 0.03
836 255 0.14
837 53 0.03
839 1 0.00
841 43 0.02
844 1 0.00
845 1 0.00
848 5 0.00
850 1 0.00
854 1 0.00
855 6 0.00
856 1 0.00
857 1 0.00
860 1 0.00
861 2 0.00
863 1 0.00
867 6 0.00
869 2 0.00
870 1 0.00
875 419 0.23
876 2 0.00
877 559 0.31
878 19 0.01
879 56 0.03
880 2 0.00
881 202 0.11
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.45
Consensus pattern (874 bp):
TTAATTTTGACATGCATTGTGGTTGAATGCTTAAAAGGAAGATTATTTCTTTTTGCTGGATTCTT
TGAAACTCTAAATATATGTTGTCATAGGCTCTCAGTTGGTGTCTTTTTCATTGAGATTGTCTCTG
GATTCTTCTTGTGTCATTTTTAAATCTTTACATAAATTAGGGCTTTGTAACTTTACTTTGGAAAA
TTCCTTGGGTTGTTCTTCCTTTAGTGTGGTTTGTGATTCGTTGGTCTCTATGAAACTTATGCGCT
ATGTGCTCCAAGAACGACTTGCAGTGTAGGGGGAATTAAGGATTCTAAAGTTGTATGTGTGTAGG
ATTTAAGGATTAAAAATTTGTGTGGCTGTGTATGGGAGTTTCCTTGTTTTTCTCTTTGTGTGCTC
TAAGCTAATGGCTTGCATGATTAGCTGAATTCAATTTCTGTGCCTGATGTGTGTGTAGGTTTTTT
GGGAGTTTTTTGTTTTGTTGATTTCACTCTTTTGTTATAGAATAGGTTGGTTTGTTGGGTTCAAT
TTCTGAAACTTAATTTTGACATGCATTGTGGTCAAATGTTTAAAAGGAAGATTATTTCCTTTTGT
TGGATTCTTTGAAACTCTAAATATGTGTATGGGAGTTTCCTTGTTGCTTTGTAGTGTAGGGGGAA
TTAAGGATTCTAAATTTCTATGGTTGTGTAGCATTTAAGGATTAAAAATTTGTGGCTGTGTGTAT
GGAAGTTTTCCTGTTGTTTTCTCCTTGTGTGCTTCAAGCAGTGAATTCAATTTCTGTGCCTCTGT
GTGTGTAGGTATGTGTTTAGGGAGGGTTTTATTTTGTTGGTTTCACTCTATTTGTTACAGGGCAG
ATTGGTTTGCTAGGTTCAATTTTTGTAAT
Found at i:15164 original size:355 final size:352
Alignment explanation
Indices: 14701--15387 Score: 1040
Period size: 355 Copynumber: 1.9 Consensus size: 352
14691 TTTCTCCTTG
* * *
14701 TGTGCTTCAAGCAGTTAATTCAATTTCTGTGCCTCTTGTGTGAGTAGGTATATGTTTAGGGAGGT
1 TGTGATTCAAGCAGTGAATTCAATTTCTGTGCCTCTTGTGTGAGTAGGTATATGTTTAGAGAGGT
* * *
14766 TTTTATTTTGTTGGTTTCACTCTATTTGTTACAGAGCAGATTGGTTTGTTAGGTTTCATTTTTGT
66 TTTTATTTTGTTAGTTTCACTCTATTTGTTACAGAGCAGATTGGTTTGCTAGGTTTAATTTTTGT
* *
14831 AATTTAATTATGACGTGCATTATGGTTGAATGCTTGAAAGGAAGATTATTTCTTTTTGCTGGATT
131 AATTTAATTATGACATGCATTATGGTTGAATGCTTAAAAGGAAGATTATTT-TTTTT-CTGGATT
*
14896 CTTTG-AAACTCTAAATATATGTTGTCATATGCTCTC-GGTGTC-TTTCTCATTGAGATTGTCTC
194 C-TTGAAAACTCTAAATATATGTTGTCATAGGCTCTCTGGTGTCTTTTCTCATTGAGATTGTCTC
*
14958 TGGATTTTTCTTGTGTCATTTTTAAATTTTTACATAAATTAGGGCTTTATAATTTTACTTT-GAA
258 TGGA---TTCTTGTGTCATTTTTAAATTTTTACATAAATTAGGGCTTTATAACTTTACTTTGGAA
15022 AATTTTCTTGGGTTATTCTTCCTTTAGTGTGGTT
320 AA-TTTCTTGGGTTATTCTTCCTTTAGTGTGGTT
* * *
15056 TGTGATTCAAGCAGTGAATTCAATTTCTGTGCCTCTTGTGTGTGTAGGTATGTGTTTAGAGATGT
1 TGTGATTCAAGCAGTGAATTCAATTTCTGTGCCTCTTGTGTGAGTAGGTATATGTTTAGAGAGGT
* *
15121 TTTTATTTTGTTAGTTTCACTCTATTTGTTACAGGGTAGATTGGTTTGCTAGGTTTAATTTTTGT
66 TTTTATTTTGTTAGTTTCACTCTATTTGTTACAGAGCAGATTGGTTTGCTAGGTTTAATTTTTGT
* * *
15186 AATTTAATTTTGACATGCATTGTGGTTGAATGCTTAAAAGTAAGATTATTTTTTTTCTGGATTCT
131 AATTTAATTATGACATGCATTATGGTTGAATGCTTAAAAGGAAGATTATTTTTTTTCTGGATTCT
*
15251 TGAAAACTCTAAATATATGTTGTCATAGGCTCTCAGTTGGTGTCTTTTTTTCATTGAGATTGTCT
196 TGAAAACTCTAAATATATGTTGTCATAGGCTCTC---TGGTGTC-TTTTCTCATTGAGATTGTCT
* * * *
15316 TTGGATTCTTGTGTTATTTTTAAATTTTTACATAATTTAGGGCTTTGTAACTTTACTTTGGAAAA
257 CTGGATTCTTGTGTCATTTTTAAATTTTTACATAAATTAGGGCTTTATAACTTTACTTTGGAAAA
15381 TTTCTTG
322 TTTCTTG
15388 AATTGACTTT
Statistics
Matches: 301, Mismatches: 23, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
352 3 0.01
353 38 0.13
354 5 0.02
355 165 0.55
356 57 0.19
357 11 0.04
359 22 0.07
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (352 bp):
TGTGATTCAAGCAGTGAATTCAATTTCTGTGCCTCTTGTGTGAGTAGGTATATGTTTAGAGAGGT
TTTTATTTTGTTAGTTTCACTCTATTTGTTACAGAGCAGATTGGTTTGCTAGGTTTAATTTTTGT
AATTTAATTATGACATGCATTATGGTTGAATGCTTAAAAGGAAGATTATTTTTTTTCTGGATTCT
TGAAAACTCTAAATATATGTTGTCATAGGCTCTCTGGTGTCTTTTCTCATTGAGATTGTCTCTGG
ATTCTTGTGTCATTTTTAAATTTTTACATAAATTAGGGCTTTATAACTTTACTTTGGAAAATTTC
TTGGGTTATTCTTCCTTTAGTGTGGTT
Found at i:26461 original size:22 final size:22
Alignment explanation
Indices: 26435--26477 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
26425 TAAATTTTCG
* *
26435 TTAATTTTAGAGATACAAATAC
1 TTAATTCTAGAAATACAAATAC
26457 TTAATTCTAGAAATACAAATA
1 TTAATTCTAGAAATACAAATA
26478 TAAATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (22 bp):
TTAATTCTAGAAATACAAATAC
Found at i:29926 original size:18 final size:18
Alignment explanation
Indices: 29895--29929 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29885 TAATCCATGA
* *
29895 GAACTGAAAGCTTTACCT
1 GAACTAAAAACTTTACCT
29913 GAACTAAAAACTTTACC
1 GAACTAAAAACTTTACC
29930 CAAAGAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (18 bp):
GAACTAAAAACTTTACCT
Found at i:30160 original size:23 final size:23
Alignment explanation
Indices: 30104--30182 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 23
30094 AAAGGGTTCA
* *
30104 GCAATGAAGGCCTAAACAGAATTCG
1 GCAATGAAAGCCTAAA-A-AAATCG
*
30129 GCAAAGAAAGCCTAAAAAAATCG
1 GCAATGAAAGCCTAAAAAAATCG
* *
30152 GCAATGAAAGCCTAAAAAAGTCA
1 GCAATGAAAGCCTAAAAAAATCG
30175 GCAATGAA
1 GCAATGAA
30183 GGCTGAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 33 0.69
24 1 0.02
25 14 0.29
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (23 bp):
GCAATGAAAGCCTAAAAAAATCG
Found at i:30361 original size:22 final size:22
Alignment explanation
Indices: 30333--30375 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
30323 TAAATCTTCG
*
30333 TTAATTCTAGGGATACAAATAC
1 TTAATTCTAGAGATACAAATAC
30355 TTAATTCTAGAGATACAAATA
1 TTAATTCTAGAGATACAAATA
30376 TAAATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATAC
Found at i:33868 original size:3 final size:3
Alignment explanation
Indices: 33860--33886 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
33850 ATAGAATATC
33860 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
33887 TCCATTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39844 original size:8 final size:8
Alignment explanation
Indices: 39831--39855 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39821 TTACAGCTGG
39831 TTGTAATC
1 TTGTAATC
39839 TTGTAATC
1 TTGTAATC
39847 TTGTAATC
1 TTGTAATC
39855 T
1 T
39856 GTATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTAATC
Found at i:39890 original size:22 final size:22
Alignment explanation
Indices: 39865--39908 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39855 TGTATATTTA
*
39865 TATTTGTATATCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
*
39887 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
39909 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATACCTAGAATTAAG
Found at i:43789 original size:22 final size:22
Alignment explanation
Indices: 43763--43806 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43753 TGTATATTTA
*
43763 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
43785 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
43807 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:46168 original size:163 final size:159
Alignment explanation
Indices: 45894--46198 Score: 477
Period size: 163 Copynumber: 1.9 Consensus size: 159
45884 TGTTAAAACC
* * * *
45894 TTCAACCATTAAGGAACTAGTAGAATGAGACAGGAAAAGGTTCTGTGGCGGTAGACCAGAAAGTA
1 TTCAACCATTAAGGAACTAGTAGAATGAGACAGAAAAAGGATCTGTGGCGATAGACCAGAAACTA
45959 TCAATTCAAGGTGGTTGATTCTTACAGGATAATGAGAATGAAAGGATCAAATCAGACTGGTTGCT
66 TCAATTCAAGGTGGTTGATTCTTACAGGATAATGAGAATGAAAGGATCAAATCAGACT-G--G-T
46024 TCTGATTATATTACTTGTCATTCTATAAACACT
127 TCTGATTATATTACTTGTCATTCTATAAACACT
* *
46057 TTCAACCATTAAGGAACTAGTAGAATGAGAGATAAAAAGGATCTGTGGCGATAGACCAGAAACTA
1 TTCAACCATTAAGGAACTAGTAGAATGAGACAGAAAAAGGATCTGTGGCGATAGACCAGAAACTA
* * *
46122 TCAATTCAAGGTGGTTGCTTGTTACAGTATAATGAGAACT-AAAGGATCAAATCAGACTGGTTCT
66 TCAATTCAAGGTGGTTGATTCTTACAGGATAATGAGAA-TGAAAGGATCAAATCAGACTGGTTCT
46186 GATTATATTACTT
130 GATTATATTACTT
46199 ATGTTTTATT
Statistics
Matches: 132, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
159 17 0.13
160 1 0.01
162 1 0.01
163 112 0.85
164 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (159 bp):
TTCAACCATTAAGGAACTAGTAGAATGAGACAGAAAAAGGATCTGTGGCGATAGACCAGAAACTA
TCAATTCAAGGTGGTTGATTCTTACAGGATAATGAGAATGAAAGGATCAAATCAGACTGGTTCTG
ATTATATTACTTGTCATTCTATAAACACT
Done.